Biology subjects

Penaud, B.

Publications and source records attributed to Penaud, B..

3 recordsLinked to original sources

bioRxiv2026

Adaptive introgression in subdivided populations leaves distinct genomic footprints under global and local selection: a case study in Ciona intestinalis

Adaptive introgression, the transfer of beneficial alleles between species through hybridization, is increasingly recognized as an important source of adaptation to novel environments. However, the theory of adaptive introgression has primarily been developed for a single panmictic population, whereas many empirical examples involve spatially subdivided populations. In such systems, a low-frequency adaptive allele may either represent the leading edge of an adaptive travelling wave or occur in a subpopulation where the introgressed allele is locally selected against. We developed a simple prediction based on the relationship between adaptive allele frequency and introgressed tract length. Simulations predict a positive correlation during an ongoing sweep of an unconditionally beneficial allele, but no correlation under local adaptation. Tract erosion provides a recombination clock for time since introgression, which also determines the distance travelled by the adaptive wave and hence allele frequency in the former, whereas allele frequency is determined by local selection in the latter. We tested this prediction in a well-characterized case of adaptive introgression, in the sea squirt Ciona intestinalis, using haplotagging to reconstruct phased genomes and local ancestry. We found no relationship between adaptive allele frequency and introgressed tract length, providing additional support for a model of local adaptation rather than ongoing global selective sweep.

genetics↗

bioRxiv2026

Parallel differentiation extends beyond chromosomal inversions to small genomic islands on a background of rampant gene flow in the European flat oyster (Ostrea edulis)

Heterogeneous genomic landscapes of differentiation can reveal evolutionary processes acting over different timescales. Whereas genetic structure in the European flat oyster, Ostrea edulis, is mainly shaped by geography, previous work suggested parallel differentiation between western and eastern Mediterranean populations and between Atlantic and North Sea populations, resulting in genetic convergence between range margin populations in some genomic regions. Here, we analyzed 27 oysters from four locations using moderate-coverage (~20X) short-read whole-genome sequencing. We first examined three known chromosomal inversions and found evidence that they predate divergence with the sister species O. chilensis. We then scanned the genome for parallel differentiation at the individual-SNP rather than sliding-window scale using the product of allele-frequency differences across the two geographic contrasts. Two of the three inversions were detected, but we also identified 12 small non-inverted genomic regions showing even stronger signals of parallel differentiation. These 'islands of parallelism' typically overlap one or a few genes, and most showed elevated dXY consistent with long-term barriers to gene flow. Two islands overlap nuclear ATP synthase subunits, while mitochondrial ATP8 shows a convergent amino-acid change, suggesting possible nuclear-nuclear and mitonuclear incompatibilities. Finally, demographic inference with heterogeneous gene flow supported post-glacial secondary contact and a lineage-based rather than geography-based population topology. Our results suggest that the genomes of O. edulis lineages have been largely porous to gene flow upon secondary contact, except for chromosomal inversions and small genomic islands. These regions likely act as barrier loci, preserving a signal of a shared evolutionary history among marginal populations that has otherwise been erased by rampant gene flow.

evolutionary biology↗

bioRxiv2025

Chromosome-level genome assemblies for the latent pine pathogen, Diplodia sapinea, reveal two rapidly evolving accessory chromosomes

Diplodia sapinea (Dothideomycetes) is a latent fungal pathogen with a global distribution that predominantly infects Pinus species. The impact of the fungus is increasing due to climate-driven range expansion and thus wide-scale disease outbreaks. With the aim of developing high quality genome resources, we generated chromosome-level genome assemblies for three D. sapinea isolates and low-coverage Illumina genome data for six additional isolates. By comparing these genome assemblies, we identified 14 core chromosomes and two accessory chromosomes (ACs) in the pathogen. The ACs encode 80 and 155 proteins, respectively, while 11374 - 11609 genes were identified in the core chromosomes. Both ACs had lower gene density and higher proportions of transposable elements compared to the core chromosomes. Sequence analysis indicated that genes on the ACs are rapidly evolving, suggesting they serve as evolutionary hotspots in the species. Sequence homology analyses suggested that the ACs were likely acquired horizontally, probably from a species in the Dothideomycetes. We designed PCR-based assays to aid in the detection of the ACs and applied these on a set of 37 isolates from 14 countries. One of the ACs was detected in 33 isolates from 13 countries, while the other AC was absent in all isolates tested. Pathogenicity trials on Pinus patula seedlings showed no correlation between the presence of ACs and isolate aggressiveness. The high-quality genomes provided here offer important resources for future research on this globally important pathogen, including the biological roles of the ACs.

genomics↗